Patchdeck is designed to work well alongside other patching methods. If you apply patches outside a Patchdeck workflow the agent will pick up the change and bring everything up-to-date in your dashboard. This also means reports you generate in your Patchdeck dashboard reflect not only patches applied through Patchdeck but include all patching methods.
You can also use Patchdeck with custom update repositories like Windows Server Update Services (WSUS) or Linux package repositories if you want tighter control over the source of your updates. Patchdeck will always use the repository that is configured in the OS of an endpoint as the source for patches. For most use cases we recommend keeping the standard repositories, e.g. Microsoft Update for Windows and the standard package repositories of your Linux distribution. Mac updates always use the official Apple repository.